Thermo Fisher Scientific Orbitrap Tribrid Series Owner's manual

Brand: Thermo Fisher Scientific

Model: Orbitrap Tribrid Series

Type: Owner's manual

Orbitrap Tribrid Series

Hardware Manual

80000-97027 Revision A June 2018

Automatic Gain Control, EASY-ETD, EASY-IC, EASY-Max NG, Fusion, ID-X, Lumos, OptaMax NG, and

Orbitrap ID-X are trademarks; Unity is a registered service mark; and Hypersil GOLD AQ, Orbitrap, Orbitrap

Fusion, Orbitrap Fusion Lumos, Pierce, Thermo Scientific, Tribrid, and Xcalibur are registered trademarks of

Thermo Fisher Scientific Inc. in the United States. Fisher Scientific is a registered trademark of Fisher Scientific

Co. in the United States.

The following are registered trademarks in the United States and other countries: COMBICON is a registered

trademark of Phoenix Contact GmbH & Co. Microsoft and Windows are registered trademarks of Microsoft

Corporation. Teflon is a registered trademark of E.I. du Pont de Nemours & Co.

The following are registered trademarks in the United States and possibly other countries: Liquinox is a

registered trademark of Alconox, Inc. MICRO-MESH is a registered trademark of Micro-Surface Finishing

Products, Inc. Nalgene is a registered trademark of Nalge Nunc International Corporation. Oerlikon Leybold

Vacuum is a registered trademark of OC Oerlikon Corporation AG. Rheodyne is a registered trademark of

IDEX Health & Science, LLC. SOGEVAC is a registered trademark of Oerlikon Leybold Vacuum. Swagelok is

a registered trademark of Swagelok Company. Tygon is a registered trademark of the division of Saint-Gobain

Performance Plastics Corporation. Upchurch Scientific is a registered trademark of IDEX Health & Science

LLC. Vespel is a registered trademark of E.I. du Pont de Nemours & Co. Viton is a registered trademark of

DuPont Performance Elastomers LLC.

Chemyx is a trademark of Chemyx Inc. MX Series II is a trademark of IDEX Health & Science, LLC.

All other trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries.

Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the

product operation. This document is copyright protected and any reproduction of the whole or any part of this

document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.

The contents of this document are subject to change without notice. All technical information in this

document is for reference purposes only. System configurations and specifications in this document supersede

all previous information received by the purchaser.

This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This

document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of

Sale shall govern all conflicting information between the two documents.

Release history: Rev A, June 2018

Software version: (Thermo) Foundation 3.1 SP5 and later, Xcalibur 4.2 and later, Tune 3.1 and later

For Research Use Only. Not for use in diagnostic procedures.

Regulatory Compliance

Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with

applicable North American and European regulations. Your system meets the applicable requirements in the

electromagnetic compatibility (EMC) and product safety standards described in this section.

Unauthorized changes that you make to your system will void regulatory compliance and may defeat the built-in

protections for your instrument. Some examples of unauthorized changes include using replacement parts or adding

components, options, or peripherals that Thermo Fisher Scientific has not qualified and authorized. Unauthorized

changes can also result in bodily injury and/or damage to your system and laboratory.

Ensure continued compliance with regulatory standards:

• Follow all installation instructions provided in the documentation that comes with your system.

• Order replacement parts (as specified in the instrument manual) and additional components, options, and periph-

erals directly from Thermo Fisher Scientific or an authorized representative.

Regulatory compliance results for the following Thermo Scientific™ mass spectrometers:

•Orbitrap Fusion Lumos

•Orbitrap Fusion and Orbitrap ID-X

Orbitrap Fusion Lumos

Low Voltage Directive 2014/35/EU

This device complies with Low Voltage Directive 2014/35/EU and the harmonized safety standard IEC/EN/CSA/

UL 61010-1, 3rd Edition.

EMC Directive 2014/30/EU and other EMC test standards

This device was tested by TÜV Rheinland of North America and complies with the following EMC standards:

47 CFR 15, Subpart B, Class A: 2015 EN 61000-3-2: 2006 + A1 + A2 EN 61000-4-5: 2006

CISPR 11: 2009 + A1 EN 61000-3-3: 2008 EN 61000-4-6: 2009

ICES-003: 2014 EN 61000-4-2: 2009 EN 61000-4-8: 2010

EN 55011: 2009 + A1 EN 61000-4-3: 2006 + A1 + A2 EN 61000-4-11: 2004

EN 61326-1: 2013 EN 61000-4-4: 2004 + A1

Orbitrap Fusion and Orbitrap ID-X

FCC Compliance Statement

Notice on the Proper Use of

Thermo Scientific Instruments

In compliance with international regulations: This instrument must be used in the manner specified by Thermo Fisher

Scientific to ensure protections provided by the instrument are not impaired. Deviations from specified instructions on

the proper use of the instrument include changes to the system and part replacement. Accordingly, order replacement

parts from Thermo Fisher Scientific or one of its authorized representatives.

Low Voltage Directive 2014/35/EU

This device complies with Low Voltage Directive 2014/35/EU and the harmonized safety standard IEC/EN/CSA/

UL 61010-1, 3rd Edition.

EMC Directive 2014/30/EU and other EMC test standards

This device was tested by TÜV Rheinland of North America and complies with the following EMC standards:

47 CFR 15, Subpart B, Class A: 2012 EN 61326-1: 2013 EN 61000-4-4: 2004 + A1

CISPR 11: 2009 + A1 EN 61000-3-2: 2006 + A1 + A2 EN 61000-4-5: 2006

AS/NZS CISPR 22: 2009 + A1 EN 61000-3-3: 2008 EN 61000-4-6: 2009

ICES-003: 2012 EN 61000-4-2: 2009 EN 61000-4-8: 2010

EN 55011: 2009 + A1 EN 61000-4-3: 2006 + A1 + A2 EN 61000-4-11: 2004

THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES. OPERATION IS SUBJECT TO THE

FOLLOWING TWO CONDITIONS: (1) THIS DEVICE MAY NOT CAUSE HARMFUL INTERFERENCE,

AND (2) THIS DEVICE MUST ACCEPT ANY INTERFERENCE RECEIVED, INCLUDING

INTERFERENCE THAT MAY CAUSE UNDESIRED OPERATION.

CAUTION Read and understand the various precautionary notes, signs, and symbols contained inside

this manual pertaining to the safe use and operation of this product before using the device.

WEEE Directive

2012/19/EU

Thermo Fisher Scientific is registered with B2B Compliance (B2Bcompliance.org.uk) in the UK and with the

European Recycling Platform (ERP-recycling.org) in all other countries of the European Union and in Norway.

If this product is located in Europe and you want to participate in the Thermo Fisher Scientific Business-to-Business

(B2B) Recycling Program, send an email request to weee.recycle@thermofisher.com with the following information:

• WEEE product class

• Name of the manufacturer or distributor (where you purchased the product)

• Number of product pieces, and the estimated total weight and volume

• Pick-up address and contact person (include contact information)

• Appropriate pick-up time

• Declaration of decontamination, stating that all hazardous fluids or material have been removed from the product

For additional information about the Restriction on Hazardous Substances (RoHS) Directive for the European Union,

search for RoHS on the Thermo Fisher Scientific European language websites.

IMPORTANT This recycling program is not for biological hazard products or for products that have been medically

contaminated. You must treat these types of products as biohazard waste and dispose of them in accordance with

your local regulations.

Thermo Scientific Orbitrap Tribrid Series Hardware Manual vii

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii

Accessing Documentation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii

Viewing the Product Manuals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiv

Accessing the Help Menu Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiv

Viewing Online User Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiv

Providing Documentation Feedback. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv

License for the 1M Option . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv

Special Notices, Symbols, and Cautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv

Model Differences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii

Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xviii

Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1

Orbitrap Tribrid Series Mass Spectrometers . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Overview of an LC/MS Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

LC/MS Functional Block Diagram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Electronic Assemblies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Controls and Indicators. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

LEDs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Power Entry Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Communications Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Cooling Fans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Chapter 2 Scan Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11

Scan Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

MS Scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

MS2 Scan and MSn Scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

SIM Scan. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Scan Rates for the Ion Trap Detector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Scan Mass-To-Charge Ratio Ranges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Resolutions for the Orbitrap Detector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Data Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Ion Polarity Modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Contents

viii Orbitrap Tribrid Series Hardware Manual Thermo Scientific

Chapter 3 Vacuum System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15

Vacuum System Functional Block Diagram . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Schematic of the Internal Gas Supply Lines. . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Inlet Gases Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Helium Regulator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Nitrogen Gas Valves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Vent Valve. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Vacuum Manifold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Vacuum Gauges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Vacuum Pumps. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Atmospheric Pressure Ionization Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

API Source Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Chapter 4 Ion Transmission and Mass Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27

Workflow for Mass Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Ion Optics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

MP00 Ion Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

MP0 Ion Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

MP1 Ion Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

Curved Linear Trap. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

Ion-Routing Multipole . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

MP3 Ion Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

DC Offset Voltages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Mass Analyzers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Quadrupole Mass Analyzer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Orbitrap Mass Analyzer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Linear Ion Trap Mass Analyzer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Ion Detection Systems. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

Chapter 5 Syringe Pump and Divert/Inject Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .43

Syringe Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

Divert/Inject Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

Configurations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

Controlling the Divert/Inject Valve. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

Chapter 6 System Shutdown, Startup, and Reset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .47

Shutting Down the System in an Emergency. . . . . . . . . . . . . . . . . . . . . . . . . . . 47

Placing the Mass Spectrometer in Standby Mode . . . . . . . . . . . . . . . . . . . . . . . 48

Turning On the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

Shutting Down the Mass Spectrometer System Completely . . . . . . . . . . . . . . . 48

Starting the System after a Complete Shutdown . . . . . . . . . . . . . . . . . . . . . . . . 50

Starting the LC System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

Starting the Data System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

Starting the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

Starting the Autosampler. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

Contents

Thermo Scientific Orbitrap Tribrid Series Hardware Manual ix

Resetting the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

Resetting Calibration Parameters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

Restarting the Data System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

On/Off Status for MS Components Under Varying Power Conditions. . . . . . . 54

Chapter 7 Daily Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .57

Before Operating the Orbitrap Tribrid Series System . . . . . . . . . . . . . . . . . . . . 58

Checking the System Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

Checking the Vacuum Pressure Levels. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

Checking the Gas Supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

After Operating the Orbitrap Tribrid Series System . . . . . . . . . . . . . . . . . . . . . 59

Flushing the Inlet Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60

Purging the Oil in the Forepump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

Emptying the Solvent Waste Container. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

Placing the System in Standby Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

Chapter 8 Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .63

Maintenance Schedule. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

Guidelines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

Tools and Supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

Maintaining the API Source Housing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

Maintaining the API Source Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68

Cleaning the Ion Sweep Cone, Spray Cone, and Ion Transfer Tube . . . . . . . 68

Removing the API Source Interface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

Cleaning the RF Lens, Exit Lens, MP00 RF Lens, and Lens L0. . . . . . . . . . . 74

Reinstalling the API Source Interface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78

Maintaining the Forepump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78

Maintaining the Air Filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

Pumping Down the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

Chapter 9 Replaceable Parts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .83

Orbitrap Tribrid Series Chemicals Kit. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83

Calibration Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84

MS Setup Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85

Performance Specification Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85

Single Mechanical Pump Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86

Dual Mechanical Pumps Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86

API Source Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87

Miscellaneous Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87

Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .89

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .95

Contents

xOrbitrap Tribrid Series Hardware Manual Thermo Scientific

Thermo Scientific Orbitrap Tribrid Series Hardware Manual xi

Figure 1. Functional block diagram of the Orbitrap Tribrid Series system . . . . . . . . . . . . . 5

Figure 2. Orbitrap Tribrid Series front panel LEDs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Figure 3. Power entry module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Figure 4. Communication connectors (left side of the MS) . . . . . . . . . . . . . . . . . . . . . . . . . 8

Figure 5. Functional block diagram of the vacuum system . . . . . . . . . . . . . . . . . . . . . . . . 16

Figure 6. Schematic of the internal gas supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Figure 7. Gas inlet ports (back of the MS) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Figure 8. Placement of the three turbomolecular pumps . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Figure 9. Thermo Scientific API source (H-ESI mode) . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Figure 10. API source interface cross section (Orbitrap Fusion and Orbitrap ID-X

MSs) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Figure 11. Exit lenses and RF lenses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Figure 12. Workflow for mass analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Figure 13. Ion transmission path for the Orbitrap Fusion Lumos Tribrid MS (with

the ETD source and UVPD options) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Figure 14. MP00 RF lens (left, Orbitrap Fusion Lumos MS) and lens L0 (right) . . . . . . . . 30

Figure 15. Multipole MP0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Figure 16. TK lens (both sides) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Figure 17. Multipole MP1 (Orbitrap Fusion Lumos MS) . . . . . . . . . . . . . . . . . . . . . . . . . . 32

Figure 18. C-trap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .32

Figure 19. Ion-routing multipole (IRM) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Figure 20. Multipole MP3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Figure 21. Quadrupole Q1, side and end views (Orbitrap Fusion and Orbitrap ID-X

MSs) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Figure 22. Dual-split gate lens (both sides) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Figure 23. Polarity of the RF and DC voltages applied to the Q1 rods . . . . . . . . . . . . . . . . 35

Figure 24. Schematic of the Orbitrap cell and an example stable ion trajectory . . . . . . . . . . 36

Figure 25. Electrodynamic squeezing of ions in the Orbitrap analyzer (r) versus the

increased field strength (z) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

Figure 26. Approximate shape of ion packets of different m/z values after the

voltages stabilize . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Figure 27. Linear ion trap (LIT) (Orbitrap Fusion and Orbitrap ID-X MSs) . . . . . . . . . . . 39

Figure 28. Assembly for the linear ion trap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Figure 29. Low pressure cell of the LIT mass analyzer in operation (representation) . . . . . . 42

Figure 30. Syringe pump setup (top view) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

Figure 31. Divert/inject valve positions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

Figure 32. Divert/inject valve plumbed as a loop injector and as a divert valve . . . . . . . . . . 46

Figures

xii Orbitrap Tribrid Series Hardware Manual Thermo Scientific

Figure 33. Modular divert/inject valve (front view) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

Figure 34. Ion sweep cone removed from the MS mount assembly . . . . . . . . . . . . . . . . . . 69

Figure 35. Ion transfer tube removal tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

Figure 36. Ion transfer tube removal tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

Figure 37. Spray cone, O-ring, ion transfer tube, and ion sweep cone . . . . . . . . . . . . . . . . 71

Figure 38. API source interface removed from the vacuum manifold (example). . . . . . . . . 73

Figure 39. Lens L0 removed from the back of the API source interface (example) . . . . . . . 74

Figure 40. MP00 RF lens assembly removed from the API source interface (example). . . . 75

Figure 41. RF lens removed from the API source interface cage (example). . . . . . . . . . . . . 75

Figure 42. Exit lens removed from the API source interface (example). . . . . . . . . . . . . . . . 76

Figure 43. Alignment slot and thumbscrew locations on the MP00 RF lens

(example) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

Figure 44. Power entry module (right side of the MS) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80

Thermo Scientific Orbitrap Tribrid Series Hardware Manual xiii

Preface

The Orbitrap Tribrid Series Hardware Manual describes the modes of operation and hardware

components for the Thermo Scientific Orbitrap™ Tribrid™ Series mass spectrometer (MS)

system. It also provides the instrument’s cleaning and maintenance procedures.

This guide is intended for the following Thermo Scientific MSs:

• Orbitrap Fusion™ (also known as Fusion™)

• Orbitrap Fusion Lumos™ (also known as Lumos™)

• Orbitrap ID-X™ (also known as ID-X™)

Contents

• Accessing Documentation

• Providing Documentation Feedback

• License for the 1M Option

• Special Notices, Symbols, and Cautions

• Model Differences

•Contacting Us

Accessing Documentation

The Orbitrap Tribrid Series MS includes complete documentation.

•Viewing the Product Manuals

•Accessing the Help Menu Options

•Viewing Online User Documentation

For system requirements, refer to the release notes on the software DVD.

Preface

xiv Orbitrap Tribrid Series Hardware Manual Thermo Scientific

Viewing the Product Manuals

The Thermo Fisher Scientific service engineer installs the instrument control applications and

the instrument manuals on the data system computer.

To view the product manuals

From the Microsoft™ Windows™ taskbar, choose Start > All Apps (Windows 10) or

All Programs (Windows 7) > Thermo Instruments > model x.x, and then open the

applicable PDF file.

Accessing the Help Menu Options

Follow this procedure to view the Help systems for the instrument-control applications.

To view the Help

Do the following as applicable:

• Thermo Tune instrument-control application: Click the Options icon, , and

choose Tu ne He l p.

• Thermo Xcalibur™ Method Editor application: Choose an option from the Help

menu (or press the F1 key).

Viewing Online User Documentation

Visit the Thermo Fisher Scientific website for product manuals and more.

To view user documentation from the Thermo Fisher Scientific website

1. Go to thermofisher.com.

2. Point to Services & Support and click Manuals on the left.

3. In the Refine Your Search box, search by the product name.

4. From the results list, click the title to open the document in your web browser, save it, or

print it.

To return to the document list, click the browser Back button.

Preface

Thermo Scientific Orbitrap Tribrid Series Hardware Manual xv

Providing Documentation Feedback

To suggest changes to the documentation or to the Help

Complete a brief survey about this document by clicking the button below.

Thank you in advance for your help.

License for the 1M Option

During the Orbitrap Fusion Lumos MS installation or upgrade process, the Thermo Fisher

Scientific field service engineer activates the optional 1M license (with purchase of the 1M

option).

Special Notices, Symbols, and Cautions

Make sure you understand the special notices, symbols, and caution labels in this guide. Most

of the special notices and cautions appear in boxes; those pertaining to safety also have

corresponding symbols. Some symbols are also marked on the instrument itself and can

appear in color or in black and white. For complete definitions, see Table 1.

Table 1. Notices, symbols, labels, and their meanings (Sheet 1 of 2)

Notice, symbol, or label Meaning

IMPORTANT Highlights information necessary to prevent damage to

software, loss of data, or invalid test results; or might contain

information that is critical for optimal performance of the

product.

Note Highlights information of general interest.

Tip Highlights helpful information that can make a task easier.

Caution: Read the cautionary information associated with this

task.

Chemical hazard: Observe safe laboratory practices and

procedures when handling chemicals. Only work with volatile

chemicals under a fume or exhaust hood. Wear gloves and other

protective equipment, as appropriate, when handling toxic,

carcinogenic, mutagenic, corrosive, or irritant chemicals. Use

approved containers and proper procedures to dispose of waste

oil and when handling wetted parts of the instrument.

Preface

xvi Orbitrap Tribrid Series Hardware Manual Thermo Scientific

Read and understand the following cautions that are specific to the shutdown of the mass

spectrometry system or to the removal of parts for cleaning.

Heavy object: The Orbitrap Tribrid Series MS, excluding its

workbench, weighs over 227 kg (500 lb). Never try to detach

and move the instrument from its workbench; you can suffer

personal injury or damage the instrument.

Hot surface: Before touching the API source assembly, allow

heated components to cool.

Pinch point: Keep hands away from the specified areas.

Risk of electric shock: This instrument uses voltages that can

cause electric shock and personal injury. Before servicing the

instrument, shut it down and disconnect it from line power.

While operating the instrument, keep covers on.

Risk of eye injury: Eye injury can occur from splattered

chemicals, airborne particles, or sharp objects. Wear safety

glasses when handling chemicals or servicing the instrument.

Risk of laser radiation—Orbitrap Fusion Lumos MS with the

optional ultraviolet photodissociation (UVPD) module only:

Failure to understand and comply with laser cautions and

operating instructions in the UVPD Module User Guide can

result in property damage or serious injuries to the user.

Sharp object: Avoid handling the tip of the syringe needle.

Trip obstacle: Be aware of cords, hoses, or other objects located

on the floor.

Table 1. Notices, symbols, labels, and their meanings (Sheet 2 of 2)

Notice, symbol, or label Meaning

CAUTION If you must turn off the MS in an emergency, turn off the main power switch

located on the right-side power panel. This switch turns off all power to the MS,

including the forepump, without harming components within the system. However, do

not use this method as part of the standard shutdown procedure. Instead, see Shutting

Down the Mass Spectrometer System Completely. To turn off the LC, autosampler, and

data system computer in an emergency, use their respective on/off switch or button.

Preface

Thermo Scientific Orbitrap Tribrid Series Hardware Manual xvii

Model Differences

This table lists the required number of forepumps and the available options for the

Orbitrap Tribrid Series MSs.

CAUTION To avoid an electrical shock, be sure to follow the instructions in Shutting

Down the Mass Spectrometer System Completely.

CAUTION Do not turn the instrument on if you suspect that it has incurred any kind of

electrical damage. Instead, disconnect the power cord and contact Thermo Fisher

Scientific technical support for a product evaluation. Do not attempt to use the

instrument until it has been evaluated. (Electrical damage might have occurred if the

system shows visible signs of damage, or has been transported under severe stress.)

CAUTION Do not disconnect the power cord at the MS while the other end is still

plugged into the electrical outlet.

CAUTION Do not place any objects (for example, the syringe pump or other containers

with liquids) on top of the instrument, unless instructed to in the documentation.

Leaking liquids might contact the electronic components and cause an electrical short

circuit.

CAUTION Hot surface. Allow heated components to cool to room temperature

(approximately 20 minutes) before servicing them.

Instrument Number of

forepumps

Available options

EASY-IC

ion source

EASY-ETD

ion source

Advanced

peak

determination

1M Orbitrap

resolution

UVPD

laser module

Orbitrap Fusion Lumos 2    

Orbitrap Fusion 1  

Orbitrap ID-X 1 

Preface

xviii Orbitrap Tribrid Series Hardware Manual Thermo Scientific

Contacting Us

Contact Email Telephone QR Codea

aYou can use your smartphone to scan a QR Code, which opens your email application or browser.

U.S. Technical Support us.techsupport.analyze@thermofisher.com (U.S.) 1 (800) 532-4752

U.S. Customer Service

and Sales

us.customer-support.analyze@thermofisher.com (U.S.) 1 (800) 532-4752

Global Support To find global contact information or customize your request

1. Go to thermofisher.com.

2. Click Contact Us, select the country, and then select the type of support

you need.

3. At the prompt, type the product name.

4. Use the phone number or complete the online form.

To find product support, knowledge bases, and resources

Go to thermofisher.com/us/en/home/technical-resources.

To find product information

Go to thermofisher.com/us/en/home/brands/thermo-scientific.

Note To provide feedback for this document, go to surveymonkey.com/s/PQM6P62 or send an email message to

Technical Publications (techpubs-lcms@thermofisher.com).

Thermo Scientific Orbitrap Tribrid Series Hardware Manual 1

Introduction

The Orbitrap Tribrid Series MS is part of the Thermo Scientific family of MSs. The

Orbitrap Tribrid Series system consists of the MS, a syringe pump, a divert/inject valve, and

the Thermo Xcalibur data system.

Contents

• Orbitrap Tribrid Series Mass Spectrometers

• Overview of an LC/MS Analysis

• LC/MS Functional Block Diagram

• Electronic Assemblies

• Controls and Indicators

• Cooling Fans

Orbitrap Tribrid Series Mass Spectrometers

See these topics:

•Orbitrap Fusion MS

•Orbitrap Fusion Lumos MS

•Orbitrap ID-X MS

For a summary of the significant differences, see Model Differences.

For descriptions of the various hardware components, see Chapter 3, “Vacuum System,”

Chapter 4, “Ion Transmission and Mass Analysis,” and Chapter 5, “Syringe Pump and

Divert/Inject Valve.”

For an MS with the ETD option (see Model Differences), refer to the EASY-ETD and

EASY-IC Ion Sources User Guide. For an Orbitrap Fusion Lumos MS with the UVPD option,

refer to the UVPD Module User Guide.

Note The “Glossary” defines some of the terms used in this manual.

1 Introduction

Orbitrap Tribrid Series Mass Spectrometers

2Orbitrap Tribrid Series Hardware Manual Thermo Scientific

Orbitrap Fusion MS

The Orbitrap Fusion is a mass spectrometer that contains three mass analyzers and includes

an external syringe pump, a divert/inject valve, and the Thermo Scientific EASY-Max NG™

API source. The instrument requires one forepump.

Orbitrap Fusion Lumos MS

The Orbitrap Fusion Lumos is a mass spectrometer that contains three mass analyzers and

includes an external syringe pump, a divert/inject valve, and the EASY-Max NG API source.

The instrument requires two forepumps.

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Thermo Fisher Scientific Orbitrap Tribrid Series Owner's manual

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Model: Orbitrap Tribrid Series

Type: Owner's manual

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Thermo Fisher Scientific Orbitrap Tribrid Series Owner's manual

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